{ "code": "SASDBK7", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins.", "publication": { "title": "Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins.", "author_list": "Fedosyuk S, Bezerra GA, Radakovics K, Smith TK, Sammito M, Bobik N, Round A, Ten Eyck LF, Djinović-Carugo K, Usón I, Skern T", "journal": "PLoS Pathog", "doi": "10.1371/journal.ppat.1006079", "pmid": "27973613", "published_date": "2016 Dec" }, "status": "released", "submitted_date": "2016-11-06", "released_date": "2016-11-23" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBK7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBK7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBK7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBK7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBK7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBK7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBK7.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "type_of_source": "X-ray synchrotron", "point_source": null, "line_collimation": null, "sample_path_length": null, "line_collimation_slitlength": null, "line_collimation_integrationwidth": null, "xray_energy": null, "beam_profile_ah": null, "beam_profile_al": null }, "sample": { "molecule": [ { "long_name": "Protein A46", "short_name": "VACV A46", "sequence": "GAQQMAFDISVNASKTINALVYFSTQQNKLVIRNEVNDTHYTVEFDRDKVVDTFISYNRHNDTI\r\nEIRGVLPEETNIGCAVNTPVSMTYLYNKYSFKLILAEYIRHRNTISGNIYSALMTLDDLA\r\nIKQYGDIDLLFNEKLKVDSDSGLFDFVNFVKDMICCDSRIVVALSSLVSKHWELTNKKYR\r\nCMALAEHISDSIPISELSRLRYNLCKYLRGHTESIEDKFDYFEDDDSSTCSAVTDRETDV", "organism": "Vaccinia virus", "uniprot_code": "P26672", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MAFDISVNASKTINALVYFSTQQNKLVIRNEVNDTHYTVEFDRDKVVDTFISYNRHNDTI\nEIRGVLPEETNIGCAVNTPVSMTYLYNKYSFKLILAEYIRHRNTISGNIYSALMTLDDLA\nIKQYGDIDLLFNEKLKVDSDSGLFDFVNFVKDMICCDSRIVVALSSLVSKHWELTNKKYR\nCMALAEHISDSIPISELSRLRYNLCKYLRGHTESIEDKFDYFEDDDSSTCSAVTDRETDV", "mw": 28.019, "total_mw": 112.076, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris-HCl, 10 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.5, "deuteration": null }, "purity_method": null, "name": "Vaccinia virus A46 protein (full-length)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Vienna, Austria", "full_name": "Medical University of Vienna", "webpage": "https://www.meduniwien.ac.at" } ], "contributor_name": "Sofiya", "contributor_surname": "Fedosyuk", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-06-25", "storage_temperature": null, "cell_temperature": 20.0, "exposure_time": 0.1, "number_of_frames": null, "wavelength": 0.09918, "sample_detector_distance": 2.867, "concentration_min": null, "concentration_max": 4.4, "sample_volume": null, "flow_rate": null, "s_min": 0.122, "s_max": 4.934, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBK7_fit1_model1_img.png", "software": "CORAL", "pdb_link": [ { "pdb_code": "4lqk", "ext_code": "4LQK", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "mix", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBK7_fit1_model1.pdb", "model_mw": 113.7, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/Comp2.log", "symmetry": "", "comment": "", "user": 176 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBK7_fit1_fit_img.png", "software": null, "chi_square_value": 0.54, "p_value": 0.0, "fit_residual_plot": "SASDBK7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBK7_fit1.fit", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBK7_fit2_model1_img.png", "software": "CORAL", "pdb_link": [ { "pdb_code": "4lqk", "ext_code": "4LQK", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "mix", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBK7_fit2_model1.pdb", "model_mw": 113.7, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/Comp1.log", "symmetry": "", "comment": "", "user": 176 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBK7_fit2_fit_img.png", "software": null, "chi_square_value": 0.59, "p_value": 0.0, "fit_residual_plot": "SASDBK7_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBK7_fit2.fit", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM v5", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle) were collected from a sample of full-length Vaccinia virus A46 protein using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS; Superdex 200 10/300 column) at the BM29 beam line on the ESRF storage ring (Grenoble, France). Data were collected using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09918 nm. The SEC mobile phase consisted of 20 mM Tris-HCl, 10 mM DTT, pH 8.5, (20°C) with a sample injection concentration of 4.4 mg/ml. Data obtained from solute-free eluates and SEC-elution peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted from the SEC-peak frames to produce the data displayed in this entry.", "tags": [], "intensity_unit": null, "experimental_mw": 113.714, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 113.714, "porod_mw_error": null, "pddf_i0": 75.37, "pddf_i0_error": 0.116, "guinier_i0": 75.53, "guinier_i0_error": 0.11, "pddf_rg": 4.32, "pddf_rg_error": 0.008, "guinier_rg": 4.27, "guinier_rg_error": 0.08, "pddf_dmax": 14.0, "pddf_dmax_error": 0.0, "porod_volume": 199.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 33, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBK7_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }